Giter Club home page Giter Club logo

neuclease's Introduction

Travis CI Status

Neuclease

Tools for computing interactive "cleaves" of agglomerated neuron fragments from a DVID server.

Install

conda install -c flyem-forge -c conda-forge neuclease

Server Launch Example

neuclease_cleave_server \
    --port 5555 \
    --merge-table /path/to/merge-table.npy \
    --primary-dvid-server emdata3:8900 \
    --primary-uuid 017a \
    --primary-labelmap-instance segmentation \
    --log-dir /path/to/logs

Example Client Request

import requests

data = { "user": "bergs",
         "body-id": 673509195,
         "port": 8900,
         "seeds": {"1": [675222237], "2": [1266560684], "3": [1142805921]},
         "server": "emdata3.int.janelia.org", # DVID server
         "uuid": "017a",
         "segmentation-instance": "segmentation",
         "mesh-instance": "segmentation_meshes_tars" }

r = requests.post('http://bergs-ws1.int.janelia.org:5556/compute-cleave', json=data)
print(r.json())

# { "assignments": {
#      "1": [675222237, 12345, ...],
#      "2": [1266560684, 23456, ...],
#      "3": [1142805921, ....] },
#   ...
# }

Optional dependency

One step in the algorithm can be sped up slightly if you install graph-tool:

conda install -c flyem-forge graph-tool

(Otherwise, networkx is used. It doesn't matter much, except for very large cleaves.)

neuclease's People

Contributors

stuarteberg avatar

Watchers

James Cloos avatar  avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.